Everything you keep saying is from the perspective of Joel. And if we use his perspective, what you say is true, it was the right moral choice to make in his mind. It was a selfish decision but it was right.
Coming from the Fireflies perspective, they were just as selfish but just as right in their actions as Joel. They didn't want to give Ellie a choice in case she said no. If she created a cure, it justifies all the horrible things they have done for 20 years or so.
In Joels mind, he justifies his actions of murdering 20+ Fireflies because he saved his "daughter".
I am looking at it from the perspective of a third party. So let's say there is a girl who is told by a group of terrorists who say that if they can study her can cure cancer. She had a sister who died of cancer the previous year, and she wants to help destroy the dreaded disease, so she agrees to go. And let's give them the benefit of the doubt and say they are right. After they take her in they tell her father she will die for this cure. He cannot see her, she cannot see him, and if he tries to stop them, he will die. She has not given consent to being sacrificed. He is to be marched out into a desert with no gear for good measure. During the struggle he stops his own kidnapping and shoots his way to the operating theater. There the doctor brandishes his scalpel at close range and threatens to kill him. He kills the doctor and takes the girl out. As he leaves the leader of the organization holds him at gunpoint before trying to negotiate for the girl again, he shoots them, puts the girl in a getaway vehicle, then comes back to finish the job to minimize the chance that the terrorists can track him down to get the girl again.
The terrorists absolutely think they are in the right. That does not MAKE them in the right. From a third-party scenario, ANYONE with an even basic understanding of ethics would side with the father. Outside of informing the father that his daughter would die and not shooting him flat out. they have made every unethical decision possible. What they believe is right in the scenario is irrelevant. They kidnapped and planned to murder a girl. If this man did what he did above, not a jury in the world would convict him. Not one.
If any of the terrorists were brought before a court and tried, they would all be guilty of kidnapping and attempted murder at the very least.
And let's make one thing clear. Joel in no definition of the word murdered the fireflies. He MIGHT be argued to have murdered Marlene, but if the term justifiable homicide is to have any meaning at all, killing the Fireflies is it. Joel's actions are justified by the scenario. Subjective morality has its limits, live, and let live requires you to actually let people live. The initiation of force pretty much robbed the fireflies of their own justification.
Why did the US didn't ask the japanese people before dropping the bomb? It's not rocket science, common!
They don't want to risk it, they are not basing their decision in Ellie's, they already have justification.
The fact that WE and JOEL know Ellie's opinion it's what's agravating. If not, Joel would have no reason to feel guilty about it nor would find the need to lie Ellie about it.
Ok, come on you can do better than that. Try harder. In a war the desired effect requires both surprise and immediacy of action. And also the US DID tell these places they were going to be bombed, so your analogy fails there as well. The ethics of war are also a very different debate. none of which apply here.
Because there isn't an answer as to why the immediacy of action was required and why the lack of consent or even knowledge was required. If Marlene was so sure that Elly would say yes then why not ask her. Even if they thought she would say no, why not ask her? Doing the surgery in a day or a week or even a month later doesn't change much in the grand scheme of things. I try not to bring it up all the time, but even ruling out all other options in a way that was believable in the narrative would have made things actually ambiguous. The fireflies acted as if immediacy was necessary, when there was no story reason that it was. Hence they via the text wanted to kill a girl after studying her for a few hours and she is the only immune person they have ever seen. They lose nothing by asking her, not one single thing. But by not doing so they also lose all chance at his being and ethical decision.
And you keep saying you know Ellie's opinion. What you are saying is the equivalent of a girl saying she'd like to bang a dude, then because she said that he is going to rape her while she is passed out on a couch. Sorry for being so crass, but that is basically the same thing. Consent actually matters in the moment. There are reasons that informed consent is the pillar of medicine. We cannot know what Elliie would have said at that moment because she was never given that chance. She assumes that she would have said yes, but that is easy to say in hindsight when the danger is not imminent. She said she didn't want it to be for nothing, that is true, but she also planned on learning swim and play guitar with Joel later. She had no reason to believe that seeing the fireflies was a death sentence, the most she had to worry bout was an extended stay, maybe a very extended one as they ran tests on her.